"""
DDA Quantification Module for Ion level Quantification.
"""
from __future__ import annotations
from typing import Dict, Tuple
import pandas as pd
from pandas import DataFrame
from proteobench.datapoint.quant_datapoint import QuantDatapoint
from proteobench.exceptions import (
ConvertStandardFormatError,
IntermediateFormatGenerationError,
ParseError,
ParseSettingsError,
QuantificationError,
)
from proteobench.io.parsing.parse_ion import load_input_file
from proteobench.io.parsing.parse_settings import ParseSettingsBuilder
from proteobench.modules.constants import MODULE_SETTINGS_DIRS
from proteobench.modules.quant.quant_base_module import QuantModule
from proteobench.score.quant.quantscores import QuantScores
from proteobench.modules.quant.benchmarking import run_benchmarking_with_timing
[docs]
class DDAQuantIonAstralModule(QuantModule):
"""
DDA Quantification Module for Ion level Quantification.
Parameters
----------
token : str
GitHub token for the user.
proteobot_repo_name : str, optional
Name of the repository for pull requests and where new points are added, by default "Proteobot/Results_quant_ion_DDA".
proteobench_repo_name : str, optional
Name of the repository where the benchmarking results will be stored, by default "Proteobench/Results_quant_ion_DDA".
Attributes
----------
module_id : str
Module identifier for configuration.
precursor_column_name: str
Level of quantification.
"""
module_id = "quant_lfq_DDA_ion_Astral"
def __init__(
self,
token: str,
proteobot_repo_name: str = "Proteobot/Results_quant_ion_DDA_Astral",
proteobench_repo_name: str = "Proteobench/Results_quant_ion_DDA_Astral",
):
"""
Initialize the DDA Quantification Module for Ion level Quantification for Astral.
Parameters
----------
token : str
GitHub token for the user.
proteobot_repo_name : str, optional
Name of the repository for pull requests and where new points are added, by default "Proteobot/Results_quant_ion_DDA".
proteobench_repo_name : str, optional
Name of the repository where the benchmarking results will be stored, by default "Proteobench/Results_quant_ion_DDA".
"""
super().__init__(
token,
proteobot_repo_name=proteobot_repo_name,
proteobench_repo_name=proteobench_repo_name,
parse_settings_dir=MODULE_SETTINGS_DIRS[self.module_id],
module_id=self.module_id,
)
self.precursor_column_name = "precursor ion"
[docs]
def is_implemented(self) -> bool:
"""
Return whether the module is fully implemented.
Returns
-------
bool
True if the module is fully implemented, False otherwise.
"""
return True
[docs]
def benchmarking(
self,
input_file_loc: any,
input_format: str,
user_input: dict,
all_datapoints: pd.DataFrame,
default_cutoff_min_prec: int = 3,
) -> tuple[DataFrame, DataFrame, DataFrame]:
"""
Main workflow of the module. Used to benchmark workflow results.
Parameters
----------
input_file_loc : any
Path to the workflow output file.
input_format : str
Format of the workflow output file.
user_input : dict
User provided parameters for plotting.
all_datapoints : pd.DataFrame
DataFrame containing all datapoints from the proteobench repo.
default_cutoff_min_prec : int
Minimum number of runs an ion has to be identified in.
Returns
-------
tuple[DataFrame, DataFrame, DataFrame]
Tuple containing the intermediate data structure, all datapoints, and the input DataFrame.
"""
result = run_benchmarking_with_timing(
input_file=input_file_loc,
input_format=input_format,
user_input=user_input,
all_datapoints=all_datapoints,
parse_settings_dir=self.parse_settings_dir,
module_id=self.module_id,
precursor_column_name=self.precursor_column_name,
default_cutoff_min_prec=default_cutoff_min_prec,
add_datapoint_func=self.add_current_data_point,
)
# Return only the first three elements (without timings)
return result[:3]
[docs]
def benchmarking_2(
self,
input_file_loc: str,
input_format: str,
user_input: dict[str, object],
all_datapoints: pd.DataFrame,
default_cutoff_min_prec: int = 3,
) -> tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame, dict[str, float]]:
"""
Main workflow of the module with timing information. Used to benchmark workflow results.
Parameters
----------
input_file_loc : str
Path to the workflow output file.
input_format : str
Format of the workflow output file.
user_input : dict[str, object]
User provided parameters for plotting.
all_datapoints : pd.DataFrame
DataFrame containing all datapoints from the proteobench repo.
default_cutoff_min_prec : int, optional
Minimum number of runs an ion has to be identified in (default is 3).
Returns
-------
tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame, dict[str, float]]
A 4-tuple containing:
- intermediate_metric_structure (pd.DataFrame)
- all_datapoints (pd.DataFrame)
- input_df (pd.DataFrame)
- timings (dict of step names to elapsed seconds)
"""
return run_benchmarking_with_timing(
input_file=input_file_loc,
input_format=input_format,
user_input=user_input,
all_datapoints=all_datapoints,
parse_settings_dir=self.parse_settings_dir,
module_id=self.module_id,
precursor_column_name=self.precursor_column_name,
default_cutoff_min_prec=default_cutoff_min_prec,
add_datapoint_func=self.add_current_data_point,
)
